(during Enemy at the Gate)
According to the Stargate Wiki, this is a tie in to SGU:
Joseph Mallozzi confirmed in his blog that the Odyssey's secret mission is Icarus Base related, thus informally introducing Stargate Universe.
Here's the direct answer from said blog entry:
flo writes: “1/Was the odissey’s secret mission from EATG a plan for something ? stargate revolution?”
Answer: Initially, Odyssey’s secret mission was tied to the search for a naquadria-rich planet capable of providing the energy needed to dial Destiny.